Error in exists(cacheKey, where = .rs.WorkingDataEnv, inherits = FALSE) :
invalid first argument
Error in assign(cacheKey, frame, .rs.CachedDataEnv) :
attempt to use zero-length variable name
Error in exists(cacheKey, where = .rs.WorkingDataEnv, inherits = FALSE) :
invalid first argument
Error in assign(cacheKey, frame, .rs.CachedDataEnv) :
attempt to use zero-length variable name
mxn10_plot <- ggplot(data = mxn10,
mapping = aes(x = pos_cum,
y = Fst,
color = as_factor(chr))) +
geom_point(alpha = 0.75, size = 0.5) +
scale_x_continuous(label = mxn10_axis_set$chr,
breaks = mxn10_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_color_manual(values = rep(c("#242b35", "#869ca8"),
unique(length(mxn10_axis_set$chr)))) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife",
subtitle = "Size 10,000 Step 2,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxn10_plot

mxn50_plot <- ggplot(data = mxn50,
mapping = aes(x = pos_cum,
y = Fst,
color = as_factor(chr))) +
geom_point(alpha = 0.75, size = 0.5) +
scale_x_continuous(label = mxn50_axis_set$chr,
breaks = mxn50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_color_manual(values = rep(c("#242b35", "#869ca8"),
unique(length(mxn50_axis_set$chr)))) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxn50_plot

### Regions of Interest ###
## Looking at Chromosomes with Fst of 0.25 or greater ##
mxn50_chr1_plot <- ggplot(data = filter(mxn50, chr == "NC_055957.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = mxn50_axis_set$chr,
breaks = mxn50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxn50_chr1_plot

mxn50_chr2_plot <- ggplot(data = filter(mxn50, chr == "NC_055958.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
scale_x_continuous(label = mxn50_axis_set$chr,
breaks = mxn50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxn50_chr2_plot

mxn50_chr3_plot <- ggplot(data = filter(mxn50, chr == "NC_055959.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
scale_x_continuous(label = mxn50_axis_set$chr,
breaks = mxn50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxn50_chr3_plot

mxn50_chr10_plot <- ggplot(data = filter(mxn50, chr == "NC_055966.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = mxn50_axis_set$chr,
breaks = mxn50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxn50_chr10_plot

mxn50_chr12_plot <- ggplot(data = filter(mxn50, chr == "NC_055968.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = mxn50_axis_set$chr,
breaks = mxn50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxn50_chr12_plot

### Chromosome 2 Spike Region ###
mxn50_spike_plot <- mxn50 %>%
filter(chr == "NC_055958.1") %>%
filter(midPos >= 16600000) %>%
filter(midPos <= 17000000) %>%
ggplot(.,
mapping = aes(x = midPos,
y = Fst,
size = Nsites)) +
geom_point(alpha = 0.75, color = "#869ca8") +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_size_continuous(range = c(0.5, 3)) +
labs(x = "Position",
y = "Fst",
title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife Chromosome 2",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxn50_spike_plot

mxg10_plot <- ggplot(data = mxg10,
mapping = aes(x = pos_cum,
y = Fst,
color = as_factor(chr))) +
geom_point(alpha = 0.75, size = 0.5) +
scale_x_continuous(label = mxg10_axis_set$chr,
breaks = mxg10_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_color_manual(values = rep(c("#242b35", "#869ca8"),
unique(length(mxg10_axis_set$chr)))) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 10,000 Step 2,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxg10_plot

mxg50_plot <- ggplot(data = mxg50,
mapping = aes(x = pos_cum,
y = Fst,
color = as_factor(chr))) +
geom_point(alpha = 0.75, size = 0.5) +
scale_x_continuous(label = mxg50_axis_set$chr,
breaks = mxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_color_manual(values = rep(c("#242b35", "#869ca8"),
unique(length(mxg50_axis_set$chr)))) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxg50_plot

### Regions of Interest ###
## Looking at the same chromosomes for MIDA vs NATLA ##
mxg50_chr1_plot <- ggplot(data = filter(mxg50, chr == "NC_055957.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = mxg50_axis_set$chr,
breaks = mxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxg50_chr1_plot

mxg50_chr2_plot <- ggplot(data = filter(mxg50, chr == "NC_055958.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
scale_x_continuous(label = mxg50_axis_set$chr,
breaks = mxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxg50_chr2_plot

mxg50_chr3_plot <- ggplot(data = filter(mxg50, chr == "NC_055959.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
scale_x_continuous(label = mxg50_axis_set$chr,
breaks = mxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxg50_chr3_plot

mxg50_chr10_plot <- ggplot(data = filter(mxg50, chr == "NC_055966.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = mxg50_axis_set$chr,
breaks = mxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxg50_chr10_plot

mxg50_chr12_plot <- ggplot(data = filter(mxg50, chr == "NC_055968.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = mxg50_axis_set$chr,
breaks = mxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxg50_chr12_plot

### Chromosome 2 Spike Region ###
mxg50_spike_plot <- mxg50 %>%
filter(chr == "NC_055958.1") %>%
filter(midPos >= 16600000) %>%
filter(midPos <= 17000000) %>%
ggplot(.,
mapping = aes(x = midPos,
y = Fst,
size = Nsites)) +
geom_point(alpha = 0.75, color = "#869ca8") +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_size_continuous(range = c(0.5, 3)) +
labs(x = "Position",
y = "Fst",
title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife Chromosome 2",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxg50_spike_plot

nxg10_plot <- ggplot(data = nxg10,
mapping = aes(x = pos_cum,
y = Fst,
color = as_factor(chr))) +
geom_point(alpha = 0.75, size = 0.5) +
scale_x_continuous(label = nxg10_axis_set$chr,
breaks = nxg10_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_color_manual(values = rep(c("#242b35", "#869ca8"),
unique(length(nxg10_axis_set$chr)))) +
labs(x = NULL,
y = "Fst",
title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 10,000 Step 2,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
nxg10_plot

nxg50_plot <- ggplot(data = nxg50,
mapping = aes(x = pos_cum,
y = Fst,
color = as_factor(chr))) +
geom_point(alpha = 0.75, size = 0.5) +
scale_x_continuous(label = nxg50_axis_set$chr,
breaks = nxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_color_manual(values = rep(c("#242b35", "#869ca8"),
unique(length(nxg50_axis_set$chr)))) +
labs(x = NULL,
y = "Fst",
title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
nxg50_plot

### Regions of Interest ###
## Looking at the same chromosomes for MIDA vs NATLA ##
nxg50_chr1_plot <- ggplot(data = filter(nxg50, chr == "NC_055957.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = nxg50_axis_set$chr,
breaks = nxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
nxg50_chr1_plot

nxg50_chr2_plot <- ggplot(data = filter(nxg50, chr == "NC_055958.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
scale_x_continuous(label = nxg50_axis_set$chr,
breaks = nxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
nxg50_chr2_plot

nxg50_chr3_plot <- ggplot(data = filter(nxg50, chr == "NC_055959.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
scale_x_continuous(label = nxg50_axis_set$chr,
breaks = nxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
nxg50_chr3_plot

nxg50_chr10_plot <- ggplot(data = filter(nxg50, chr == "NC_055966.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = nxg50_axis_set$chr,
breaks = nxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
nxg50_chr10_plot

nxg50_chr12_plot <- ggplot(data = filter(nxg50, chr == "NC_055968.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = nxg50_axis_set$chr,
breaks = nxg50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
nxg50_chr12_plot

### Chromosome 2 Spike Region ###
nxg50_spike_plot <- nxg50 %>%
filter(chr == "NC_055958.1") %>%
filter(midPos >= 16600000) %>%
filter(midPos <= 17000000) %>%
ggplot(.,
mapping = aes(x = midPos,
y = Fst,
size = Nsites)) +
geom_point(alpha = 0.75, color = "#869ca8") +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_size_continuous(range = c(0.5, 3)) +
labs(x = "Position",
y = "Fst",
title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife Chromosome 2",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
nxg50_spike_plot

mxf10_plot <- ggplot(data = mxf10,
mapping = aes(x = pos_cum,
y = Fst,
color = as_factor(chr))) +
geom_point(alpha = 0.75, size = 0.5) +
scale_x_continuous(label = mxf10_axis_set$chr,
breaks = mxf10_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_color_manual(values = rep(c("#242b35", "#869ca8"),
unique(length(mxf10_axis_set$chr)))) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife",
subtitle = "Size 10,000 Step 2,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxf10_plot

mxf50_plot <- ggplot(data = mxf50,
mapping = aes(x = pos_cum,
y = Fst,
color = as_factor(chr))) +
geom_point(alpha = 0.75, size = 0.5) +
scale_x_continuous(label = mxf50_axis_set$chr,
breaks = mxf50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_color_manual(values = rep(c("#242b35", "#869ca8"),
unique(length(mxf50_axis_set$chr)))) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxf50_plot

### Regions of Interest ###
## Looking at the same chromosomes for MIDA vs NATLA ##
mxf50_chr1_plot <- ggplot(data = filter(mxf50, chr == "NC_055957.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = mxf50_axis_set$chr,
breaks = mxf50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxf50_chr1_plot

mxf50_chr2_plot <- ggplot(data = filter(mxf50, chr == "NC_055958.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
scale_x_continuous(label = mxf50_axis_set$chr,
breaks = mxf50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxf50_chr2_plot

mxf50_chr3_plot <- ggplot(data = filter(mxf50, chr == "NC_055959.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
scale_x_continuous(label = mxf50_axis_set$chr,
breaks = mxf50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxf50_chr3_plot

mxf50_chr10_plot <- ggplot(data = filter(mxf50, chr == "NC_055966.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = mxf50_axis_set$chr,
breaks = mxf50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxf50_chr10_plot

mxf50_chr12_plot <- ggplot(data = filter(mxf50, chr == "NC_055968.1"),
mapping = aes(x = pos_cum,
y = Fst)) +
geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
scale_x_continuous(label = mxf50_axis_set$chr,
breaks = mxf50_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
labs(x = NULL,
y = "Fst",
title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxf50_chr12_plot

### Chromosome 2 Spike Region ###
mxf50_spike_plot <- mxf50 %>%
filter(chr == "NC_055958.1") %>%
filter(midPos >= 16600000) %>%
filter(midPos <= 17000000) %>%
ggplot(.,
mapping = aes(x = midPos,
y = Fst,
size = Nsites)) +
geom_point(alpha = 0.75, color = "#869ca8") +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_size_continuous(range = c(0.5, 3)) +
labs(x = "Position",
y = "Fst",
title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife Chromosome 2",
subtitle = "Size 50,000 Step 10,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
mxf50_spike_plot

nxf10_plot <- ggplot(data = nxf10,
mapping = aes(x = pos_cum,
y = Fst,
color = as_factor(chr))) +
geom_point(alpha = 0.75, size = 0.5) +
scale_x_continuous(label = nxf10_axis_set$chr,
breaks = nxf10_axis_set$center) +
scale_y_continuous(expand = c(0,0),
limits = c(-0.05, 1)) +
scale_color_manual(values = rep(c("#242b35", "#869ca8"),
unique(length(nxf10_axis_set$chr)))) +
labs(x = NULL,
y = "Fst",
title = "N. Atlantic Anadromous vs Finger Lakes Landlocked Alewife",
subtitle = "Size 10,000 Step 2,000") +
theme_bw() +
theme(legend.position = "none",
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.y = element_markdown(),
axis.text.x = element_text(angle = 90,
size = 8,
vjust = 0.5))
nxf10_plot
